Freiburg RNA Tools
NIPU - Help
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Introduction

This server allows to display splicing regulatory motifs and single-stranded regions.

For splicing regulatory motifs, we use the NI scores (see Stadler et al. (2006)). A hexamer with a positive NI score is considered to have ESE function, a hexamer with a negative NI score is considered to have ESS function. Strong ESEs have a score > 0.8, strong ESS a score < -0.8. Hexamers with a score between -0.8 and 0.8 are considered to be splicing-neutral, since their splicing effect is predicted to be weak.

For single-stranded regions, we compute the probability that a hexamer is completely unpaired (denoted as the PU value). PU values range between 0 (hexamer is completely base-paired) and 1 (hexamer is completely unpaired). The PU value for one hexamer is determined as the average of all local folding windows that comprise a context up- and downstream of 11 to 30 nt. PU value computations are based on RNAfold from the Vienna RNA package.
NOTE: For analyzing an entire exon, you have to input the exon sequence as well as 30 nt from its upstream and downstream intron flank.

The procedure to compute PU values is illustrated in this figure.

Note: the NIPU tool is not maintained anymore.

When using NIPU please cite :

Results are computed with NIPU version 1.0.1 using Vienna RNA package v2.1.8

Overview

The following parameters are used to control the execution of NIPU

Furthermore, additional information is available

Sequence Parameters

?  RNA sequence 1

The single RNA sequence has to be provided without header etc. At least 66 nt are needed (30 nt up- and downstream and 6 nt for one hexamer).
The parameter constraints are: Has to be an RNA sequence of the alphabet {ACGTUacgtu}. String length has to be in range (66,2000). Maximally 1 line is allowed.

?  RNA sequence 2

The single RNA sequence has to be provided without header etc. At least 66 nt are needed (30 nt up- and downstream and 6 nt for one hexamer).
The parameter constraints are: Has to be an RNA sequence of the alphabet {ACGTUacgtu}. String length has to be in range (66,2000). Maximally 1 line is allowed.

Output Description

The first plot shows the NI scores for the sequence(s), the second plot the PU values. Furthermore, the individual PU values are listed per sequence position.

Input Examples

?  human CFTR exon 12

The upper case letters are human CFTR exon 12, lower case letters 30 nt intronic flanks.
The example's result can be directly accessed here

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